Alexa Fluor 488 NHS ester | 1026613-31-9

• 分子结构分类: 有机化合物 - 有机杂环化合物 - 苯并吡喃
• 英文名称: Alexa Fluor 488 NHS ester
• 英文别名: 2-(3-Amino-6-imino-4,5-disulfoxanthen-9-yl)-4-(2,5-dioxopyrrolidin-1-yl)oxycarbonylbenzoic acid
• CAS: 1026613-31-9
• 化学式: C₂₅H₁₇N₃O₁₃S₂
• 分子量: 631.554
• InChiKey: YKLGJTAEYLITDR-UHFFFAOYSA-N

物化性质

• 密度：
  1.91±0.1 g/cm3(Predicted)

计算性质

• 辛醇/水分配系数(LogP)：
  1.68
• 重原子数：
  43.0
• 可旋转键数：
  6.0
• 环数：
  5.0
• sp3杂化的碳原子比例：
  0.08
• 拓扑面积：
  272.73
• 氢给体数：
  5.0
• 氢受体数：
  12.0

反应信息

• 作为反应物：
  描述：

  [[(2R,3S,5R)-3-[(E)-7-aminohept-2-enoxy]-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl] phosphono hydrogen phosphate 、 Alexa Fluor 488 NHS ester 以 aq. phosphate buffer 、 二甲基亚砜 为溶剂， 生成
  参考文献：
  名称：

  Synthesis of 3′-O-fluorescently mono-modified reversible terminators and their uses in sequencing-by-synthesis

  摘要：

  Next-generation sequencing (NGS) technologies recently developed are now used for study of genomes from various organisms. Sequencing-by-synthesis (SBS) is a key strategy in the NGS. The SBS uses nucleotides so-called dual-modified reversible terminators (DRTs) in which bases are labeled with fluorophores and 3'-OH is protected with a reversibly cleavable chemical group, respectively. In this study, we examined the possibility of performing SBS with mono-modified reversible terminators (MRTs), in which the reversible blocking group on the 3'-OH plays a dual role as a fluorescent signal report as well as a chemical protection. We studied cyclic reversible termination by using two MRTs (dA and dT), wherein the modifications were two different fluorophores and cleavable to regenerate a free 3'-OH. We here demonstrated that SBS could be achieved with incorporation of MRTs by a DNA polymerase and correct base-calls based on the two different colors from the fluorophores. (C) 2013 Elsevier Ltd. All rights reserved.

  DOI：

  10.1016/j.bmcl.2013.11.040

文献信息

• Photophysical Properties and Synthesis of New Dye–Cyclooctyne Conjugates for Multicolor and Advanced Microscopy
  作者：Anna Hörner、Tobias Hagendorn、Ute Schepers、Stefan Bräse

  DOI：10.1021/acs.bioconjchem.5b00059

  日期：2015.4.15

  Cyclooctyne conjugates with fluorophores are often used for bioorthogonal labeling in cells and tissues. However, no comprehensive library of one cyclooctyne core structure with different fluorescent dyes spanning the whole visible spectrum up to the NIR had been described so far. Hence, we synthesized and evaluated one cyclooctyne core structure which is easily accessible for the attachment of different dyes for multicolor imaging, FRET analysis, and study of metabolism in vivo. For these reasons we developed an easy one step synthesis starting from a known cyclooctyne. In combination with NHS-activated dyes, the cyclooctyne reacted to the dye DAB-MFCO conjugates within only 1–2 h at room temperature with high yields. We created conjugates with dyes that have high brightness and are bleaching stable with wavelengths from green to NIR. The ability to label glycans on cell surfaces was tested. All dye DAB-MFCO conjugates undergo click reactions on azide functionalized glycan structures with satisfactory photophysical properties. In total, seven different dye DAB-MFCO conjugates were synthesized; their photophysical properties and suitability for click labeling in biological applications were evaluated, making them suitable for single molecule and high resolution measurements.

  带有荧光团的环辛炔共轭物通常用于细胞和组织的生物正交标记。然而，迄今为止还没有描述过一个具有不同荧光染料的环辛炔核心结构的综合库，其范围涵盖整个可见光谱直至近红外光谱。因此，我们合成并评估了一种环辛炔核心结构，它很容易连接不同的染料，用于多色成像、FRET 分析和体内代谢研究。因此，我们从已知的环辛炔开始，开发了一种简单的一步合成方法。环辛炔与 NHS 激活的染料结合后，在室温下仅需 1-2 小时就能与染料 DAB-MFCO 共轭体发生反应，而且产量很高。我们制备的染料共轭物具有高亮度和漂白稳定性，波长从绿色到近红外。我们还测试了标记细胞表面聚糖的能力。所有染料 DAB-MFCO 共轭物都能在叠氮化物功能化的聚糖结构上发生点击反应，并具有令人满意的光物理特性。总共合成了七种不同的染料 DAB-MFCO 共轭物；评估了它们的光物理特性以及在生物应用中进行单击标记的适宜性，使它们适用于单分子和高分辨率测量。
• A Tri<i>PPP</i>ro‐Nucleotide Reporter with Optimized Cell‐Permeable Dyes for Metabolic Labeling of Cellular and Viral DNA in Living Cells
  作者：Vincente T. Sterrenberg、Dörte Stalling、J. Iven H. Knaack、Timothy K. Soh、Jens B. Bosse、Chris Meier

  DOI：10.1002/anie.202308271

  日期：2023.9.18

  The metabolic labeling of nucleic acids in living cells is highly desirable to track the dynamics of nucleic acid metabolism in real‐time and has the potential to provide novel insights into cellular biology as well as pathogen‐host interactions. Catalyst‐free inverse electron demand Diels–Alder reactions (iEDDA) with nucleosides carrying highly reactive moieties such as axial 2‐trans‐cyclooctene (2TCOa) would be an ideal tool to allow intracellular labeling of DNA. However, cellular kinase phosphorylation of the modified nucleosides is needed after cellular uptake as triphosphates are not membrane permeable. Unfortunately, the narrow substrate window of most endogenous kinases limits the use of highly reactive moieties. Here, we apply our TriPPPro (triphosphate pronucleotide) approach to directly deliver a highly reactive 2TCOa‐modified 2′‐deoxycytidine triphosphate reporter into living cells. We show that this nucleoside triphosphate is metabolically incorporated into de novo synthesized cellular and viral DNA and can be labeled with highly reactive and cell‐permeable fluorescent dye‐tetrazine conjugates via iEDDA to visualize DNA in living cells directly. Thus, we present the first comprehensive method for live‐cell imaging of cellular and viral nucleic acids using a two‐step labeling approach.

  摘要 对活细胞中的核酸进行代谢标记非常有助于实时跟踪核酸代谢的动态，并有可能为细胞生物学以及病原体与宿主之间的相互作用提供新的见解。与携带高活性分子（如轴向 2-反式环辛烯（2TCOa））的核苷进行的无催化剂反电子需求 Diels-Alder 反应（iEDDA）是实现 DNA 细胞内标记的理想工具。然而，由于三磷酸盐不具有膜渗透性，因此细胞摄取后需要细胞激酶对修饰的核苷进行磷酸化。遗憾的是，大多数内源性激酶的底物窗口狭窄，限制了高活性分子的使用。在这里，我们采用 TriPPPro（三磷酸代核苷酸）方法将高活性的 2TCOa 修饰的 2′-脱氧胞苷三磷酸报告物直接输送到活细胞中。我们的研究表明，这种三磷酸核苷可通过新陈代谢结合到新合成的细胞和病毒 DNA 中，并可通过 iEDDA 用高活性和细胞渗透性荧光染料-四嗪共轭物进行标记，从而直接观察活细胞中的 DNA。因此，我们首次提出了利用两步标记法对细胞和病毒核酸进行活细胞成像的综合方法。
• Multicolor, Cell-Impermeable, and High Affinity BACE1 Inhibitor Probes Enable Superior Endogenous Staining and Imaging of Single Molecules
  作者：Florian Stockinger、Pascal Poc、Alexander Möhwald、Sandra Karch、Stephanie Häfner、Christian Alzheimer、Guillaume Sandoz、Tobias Huth、Johannes Broichhagen

  DOI：10.1021/acs.jmedchem.4c00339

  日期：2024.6.27

  the dyes′ labeling capabilities in overexpressing cell systems and in native neuronal tissue. With multiple colors at hand, we evaluated BACE1-multimerization by Förster resonance energy transfer (FRET) acceptor-photobleaching and single-particle imaging of native BACE1. In summary, our novel fluorescent inhibitors, termed Alexa-C3, offer unprecedented insights into protein–protein interactions and

  流行但并非无可争议的淀粉样蛋白级联假说将 APP 裂解酶 1 (BACE1) 的 β 位点置于阿尔茨海默病发病机制的中心位置。在这里，我们使用新颖的无标签和无抗体标记工具研究了 BACE1 的功能特性，这些工具是与不同的不可渗透的 Alexa Fluor 染料连接的 BACE1 抑制剂 IV（也称为 C3）的缀合物。我们证明这些荧光小分子与 BACE1 特异性结合，在其正构位点具有 1:1 的标记化学计量。这是一个至关重要的特性，特别是对于单分子和超分辨率显微镜方法来说，可以表征染料在过表达细胞系统和天然神经元组织中的标记能力。有了多种颜色，我们通过福斯特共振能量转移 (FRET) 受体光漂白和天然 BACE1 的单粒子成像来评估 BACE1 多聚化。总之，我们的新型荧光抑制剂（称为Alexa-C3 ）为 BACE1 的蛋白质相互作用和扩散行为提供了前所未有的见解，直至单分子水平。
• 芳基化偶联剂、荧光染料偶联物及相关应用
  申请人：北京大学

  公开号：CN116768816A

  公开（公告）日：2023-09-19

  本发明提供了一种芳基化偶联剂、荧光染料偶联物及相关应用。该芳基化偶联剂具有如下结构式：#imgabs0#R1为H或氨基的保护基；R2选自烷基；R3选自取代或未取代的亚芳基、亚烷基、杂亚烷基或杂亚环烯基，当R3含有取代基时，取代基位于亚芳基、亚烷基或杂亚环烯基的任意可取代的位置，取代基选自含或不含杂原子的C1～C6的烷基、卤素、氨基及硝基中的任意一种或多种，杂亚环烯基或含有杂原子的C1～C6的烷基中的杂原子各自独立地选自O、S或N，杂原子位于任意一个碳原子的位置；X为F或Cl。在相同条件下，此类芳基化偶联剂与染料偶联反应速度快，且形成的产物比马来酰亚胺的反应产物更为稳定。
• COLOR-ENCODING AND IN-SITU INTERROGATION OF MATRIX-COUPLED CHEMICAL COMPOUNDS
  申请人：BioArray Solutions Ltd.

  公开号：EP1003904B1

  公开（公告）日：2007-07-11